Diane-
  Thanks for the sample images. These are not traditional T1 scans, but rather these are the Siemens *fl3d1_ns "AAHead_Scout" sequence. As dcm2niix notes when converting this image, this series can not be converted to a traditional NIfTI image since not all slices are in the same plane (some are coronal, others axial and most sagittal) and the distance between slices in the same plane are not equidistant. These scans are specifically designed for the the AutoAlign planning. I never export my localizer scans. I suggest you discard these initial planning scans. 


To ease your burden, I have updated the software so that if you choose the 'i'gnore option ("-i y") images of the type *fl3d1_ns will not be exported. 
https://github.com/rordenlab/dcm2niix/co...